Starting phenix.real_space_refine on Mon Mar 11 18:47:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijb_35484/03_2024/8ijb_35484_neut_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5632 2.51 5 N 1506 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2301 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1712 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8842 At special positions: 0 Unit cell: (91.8, 121.55, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1638 8.00 N 1506 7.00 C 5632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=1.91 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 31.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 26 through 54 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 61 through 88 removed outlier: 3.823A pdb=" N PHE A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 98 through 129 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 141 through 162 removed outlier: 4.532A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 217 removed outlier: 3.743A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 272 through 293 removed outlier: 3.667A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 30 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 208 through 215 removed outlier: 5.001A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE C 215 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.927A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.218A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 181 removed outlier: 4.477A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.970A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.832A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 335 through 339 removed outlier: 3.956A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.728A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.838A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER S 120 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.856A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 146 372 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2300 1.33 - 1.45: 1880 1.45 - 1.58: 4758 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9033 Sorted by residual: bond pdb=" N04 OJX A 401 " pdb=" O01 OJX A 401 " ideal model delta sigma weight residual 1.404 1.245 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" N PRO A 168 " pdb=" CD PRO A 168 " ideal model delta sigma weight residual 1.473 1.560 -0.087 1.40e-02 5.10e+03 3.89e+01 bond pdb=" CG ASN A 45 " pdb=" OD1 ASN A 45 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.59e+01 bond pdb=" CG ASN A 68 " pdb=" OD1 ASN A 68 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CG ASN A 68 " pdb=" ND2 ASN A 68 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.21e+01 ... (remaining 9028 not shown) Histogram of bond angle deviations from ideal: 77.24 - 91.47: 13 91.47 - 105.69: 170 105.69 - 119.92: 7851 119.92 - 134.14: 4203 134.14 - 148.37: 6 Bond angle restraints: 12243 Sorted by residual: angle pdb=" N TYR A 294 " pdb=" CA TYR A 294 " pdb=" C TYR A 294 " ideal model delta sigma weight residual 111.40 145.47 -34.07 1.22e+00 6.72e-01 7.80e+02 angle pdb=" N SER A 297 " pdb=" CA SER A 297 " pdb=" CB SER A 297 " ideal model delta sigma weight residual 114.17 139.03 -24.86 1.14e+00 7.69e-01 4.76e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 110.41 85.44 24.97 1.23e+00 6.61e-01 4.12e+02 angle pdb=" C ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta sigma weight residual 110.42 148.37 -37.95 1.99e+00 2.53e-01 3.64e+02 angle pdb=" N PHE C 323 " pdb=" CA PHE C 323 " pdb=" C PHE C 323 " ideal model delta sigma weight residual 108.75 77.24 31.51 1.71e+00 3.42e-01 3.40e+02 ... (remaining 12238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4458 18.00 - 35.99: 622 35.99 - 53.99: 199 53.99 - 71.98: 42 71.98 - 89.98: 17 Dihedral angle restraints: 5338 sinusoidal: 2047 harmonic: 3291 Sorted by residual: dihedral pdb=" C ASN A 171 " pdb=" N ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta harmonic sigma weight residual -122.60 -159.28 36.68 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" N TYR A 295 " pdb=" C TYR A 295 " pdb=" CA TYR A 295 " pdb=" CB TYR A 295 " ideal model delta harmonic sigma weight residual 122.80 92.90 29.90 0 2.50e+00 1.60e-01 1.43e+02 dihedral pdb=" N ASN B 35 " pdb=" C ASN B 35 " pdb=" CA ASN B 35 " pdb=" CB ASN B 35 " ideal model delta harmonic sigma weight residual 122.80 94.30 28.50 0 2.50e+00 1.60e-01 1.30e+02 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 1368 0.293 - 0.585: 10 0.585 - 0.878: 4 0.878 - 1.170: 2 1.170 - 1.463: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR A 294 " pdb=" N TYR A 294 " pdb=" C TYR A 294 " pdb=" CB TYR A 294 " both_signs ideal model delta sigma weight residual False 2.51 1.05 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.37 2.00e-01 2.50e+01 4.72e+01 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 1.60 1.12 2.00e-01 2.50e+01 3.15e+01 ... (remaining 1383 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -1.102 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 128 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG A 228 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " -0.100 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 284 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.110 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 96 2.52 - 3.11: 6742 3.11 - 3.71: 13526 3.71 - 4.30: 18489 4.30 - 4.90: 31563 Nonbonded interactions: 70416 Sorted by model distance: nonbonded pdb=" O HIS A 259 " pdb=" CG HIS A 259 " model vdw 1.921 3.260 nonbonded pdb=" O ASN A 86 " pdb=" O ARG A 89 " model vdw 1.936 3.040 nonbonded pdb=" O SER A 297 " pdb=" OG SER A 297 " model vdw 1.966 2.440 nonbonded pdb=" N PHE C 323 " pdb=" O PHE C 323 " model vdw 1.998 2.496 nonbonded pdb=" N PHE A 296 " pdb=" O PHE A 296 " model vdw 2.067 2.496 ... (remaining 70411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.130 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 9033 Z= 0.410 Angle : 1.536 37.949 12243 Z= 0.973 Chirality : 0.107 1.463 1386 Planarity : 0.021 0.494 1554 Dihedral : 19.136 89.979 3195 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.30 % Favored : 91.43 % Rotamer: Outliers : 8.31 % Allowed : 35.86 % Favored : 55.84 % Cbeta Deviations : 1.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1120 helix: 0.53 (0.30), residues: 357 sheet: -0.40 (0.33), residues: 270 loop : -2.16 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 50 HIS 0.002 0.000 HIS A 223 PHE 0.031 0.001 PHE A 193 TYR 0.110 0.002 TYR A 284 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 180 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 284 TYR cc_start: 0.7799 (m-80) cc_final: 0.7566 (m-80) REVERT: A 285 MET cc_start: 0.7792 (ptp) cc_final: 0.7385 (pmm) REVERT: A 290 ASP cc_start: 0.7957 (m-30) cc_final: 0.7733 (m-30) REVERT: B 130 GLU cc_start: 0.8940 (mp0) cc_final: 0.8635 (mp0) REVERT: C 197 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8312 (mttt) REVERT: S 18 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6452 (ttp80) outliers start: 79 outliers final: 40 residues processed: 234 average time/residue: 0.2313 time to fit residues: 72.4520 Evaluate side-chains 201 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 130 GLN Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 210 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS B 35 ASN B 75 GLN C 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9033 Z= 0.247 Angle : 0.596 8.002 12243 Z= 0.312 Chirality : 0.042 0.219 1386 Planarity : 0.005 0.077 1554 Dihedral : 8.150 80.155 1289 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.73 % Allowed : 33.12 % Favored : 60.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1120 helix: 1.56 (0.28), residues: 365 sheet: -0.44 (0.32), residues: 273 loop : -1.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.010 0.001 HIS A 184 PHE 0.012 0.001 PHE C 189 TYR 0.019 0.001 TYR A 87 ARG 0.011 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 170 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.6027 (m-40) REVERT: A 264 GLN cc_start: 0.8738 (tp40) cc_final: 0.8376 (tp40) REVERT: A 290 ASP cc_start: 0.8318 (m-30) cc_final: 0.8087 (m-30) REVERT: B 134 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8158 (ptp90) REVERT: B 338 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8541 (mm) REVERT: C 294 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.7942 (t0) REVERT: S 3 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7613 (mm110) REVERT: S 18 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6866 (tpp80) REVERT: S 65 LYS cc_start: 0.8397 (mttp) cc_final: 0.8001 (mttp) outliers start: 64 outliers final: 36 residues processed: 214 average time/residue: 0.2335 time to fit residues: 66.9183 Evaluate side-chains 194 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9033 Z= 0.372 Angle : 0.626 8.451 12243 Z= 0.326 Chirality : 0.044 0.193 1386 Planarity : 0.004 0.060 1554 Dihedral : 6.422 69.352 1246 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 8.94 % Allowed : 31.76 % Favored : 59.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1120 helix: 2.19 (0.28), residues: 364 sheet: -0.49 (0.32), residues: 271 loop : -1.71 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 50 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.002 PHE A 232 TYR 0.022 0.002 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 162 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8688 (t80) cc_final: 0.8385 (t80) REVERT: A 175 ASN cc_start: 0.5905 (OUTLIER) cc_final: 0.5691 (m-40) REVERT: A 264 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8430 (tp40) REVERT: A 290 ASP cc_start: 0.8297 (m-30) cc_final: 0.7953 (m-30) REVERT: B 36 ASN cc_start: 0.8261 (m110) cc_final: 0.7958 (m-40) REVERT: B 134 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8183 (ptp90) REVERT: C 294 ASN cc_start: 0.8893 (m-40) cc_final: 0.8290 (t0) REVERT: S 3 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7587 (mm110) REVERT: S 38 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7970 (ptp-170) REVERT: S 148 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6832 (ttp-170) outliers start: 85 outliers final: 60 residues processed: 228 average time/residue: 0.2333 time to fit residues: 70.9075 Evaluate side-chains 226 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 161 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9033 Z= 0.215 Angle : 0.569 8.485 12243 Z= 0.296 Chirality : 0.042 0.185 1386 Planarity : 0.004 0.057 1554 Dihedral : 6.069 67.853 1246 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.15 % Allowed : 32.39 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1120 helix: 2.48 (0.28), residues: 363 sheet: -0.59 (0.31), residues: 282 loop : -1.59 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 50 HIS 0.003 0.001 HIS A 184 PHE 0.011 0.001 PHE C 189 TYR 0.017 0.001 TYR S 178 ARG 0.009 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 166 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.9280 (t0) cc_final: 0.8530 (m-30) REVERT: A 176 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8808 (tp) REVERT: A 264 GLN cc_start: 0.8777 (tp40) cc_final: 0.8510 (tp40) REVERT: A 290 ASP cc_start: 0.8327 (m-30) cc_final: 0.7982 (m-30) REVERT: B 36 ASN cc_start: 0.8292 (m110) cc_final: 0.7956 (m-40) REVERT: B 134 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8121 (ptp90) REVERT: B 260 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: C 294 ASN cc_start: 0.8867 (m-40) cc_final: 0.8118 (t0) REVERT: S 3 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7612 (mm110) outliers start: 68 outliers final: 47 residues processed: 218 average time/residue: 0.2290 time to fit residues: 67.4451 Evaluate side-chains 210 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 75 GLN C 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9033 Z= 0.240 Angle : 0.576 8.565 12243 Z= 0.298 Chirality : 0.042 0.182 1386 Planarity : 0.004 0.061 1554 Dihedral : 5.644 62.405 1238 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 7.36 % Allowed : 32.18 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1120 helix: 2.56 (0.28), residues: 363 sheet: -0.55 (0.31), residues: 281 loop : -1.62 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.004 0.001 HIS A 184 PHE 0.012 0.001 PHE C 189 TYR 0.018 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 158 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.9240 (t0) cc_final: 0.8511 (m-30) REVERT: A 264 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (tp40) REVERT: A 290 ASP cc_start: 0.8318 (m-30) cc_final: 0.8016 (m-30) REVERT: B 36 ASN cc_start: 0.8338 (m110) cc_final: 0.7981 (m-40) REVERT: B 134 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: B 260 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: B 262 MET cc_start: 0.8783 (ttm) cc_final: 0.8560 (mtp) REVERT: B 338 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8398 (mm) REVERT: C 294 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8148 (t0) REVERT: G 21 MET cc_start: 0.7522 (mmp) cc_final: 0.7255 (mmp) REVERT: S 3 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7629 (mm110) REVERT: S 148 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6874 (ttp-170) REVERT: S 212 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8688 (t) outliers start: 70 outliers final: 56 residues processed: 208 average time/residue: 0.2262 time to fit residues: 63.6129 Evaluate side-chains 217 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 154 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 212 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 259 HIS B 88 ASN C 294 ASN C 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 9033 Z= 0.522 Angle : 0.680 9.677 12243 Z= 0.358 Chirality : 0.046 0.152 1386 Planarity : 0.004 0.055 1554 Dihedral : 5.979 55.840 1238 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.21 % Favored : 91.61 % Rotamer: Outliers : 8.94 % Allowed : 30.60 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1120 helix: 2.42 (0.28), residues: 355 sheet: -0.80 (0.31), residues: 293 loop : -1.61 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 50 HIS 0.015 0.001 HIS A 184 PHE 0.017 0.002 PHE B 241 TYR 0.025 0.002 TYR S 178 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 152 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.9253 (t0) cc_final: 0.8505 (m-30) REVERT: A 264 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (tp40) REVERT: A 290 ASP cc_start: 0.8306 (m-30) cc_final: 0.7980 (m-30) REVERT: B 36 ASN cc_start: 0.8446 (m110) cc_final: 0.8073 (m-40) REVERT: B 134 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8209 (ptp90) REVERT: B 260 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: B 338 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8510 (mm) REVERT: C 294 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8290 (t0) REVERT: S 38 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8050 (ptp-170) REVERT: S 148 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6723 (ttp-170) REVERT: S 180 MET cc_start: 0.8592 (ptm) cc_final: 0.8246 (ptm) outliers start: 85 outliers final: 65 residues processed: 217 average time/residue: 0.2206 time to fit residues: 63.8854 Evaluate side-chains 223 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 151 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 88 ASN C 294 ASN C 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9033 Z= 0.227 Angle : 0.585 9.264 12243 Z= 0.302 Chirality : 0.042 0.149 1386 Planarity : 0.004 0.053 1554 Dihedral : 5.655 56.591 1238 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.05 % Allowed : 33.33 % Favored : 59.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1120 helix: 2.57 (0.28), residues: 356 sheet: -0.59 (0.31), residues: 281 loop : -1.66 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 50 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE B 241 TYR 0.017 0.001 TYR S 178 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 162 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.9219 (t0) cc_final: 0.8519 (m-30) REVERT: A 290 ASP cc_start: 0.8278 (m-30) cc_final: 0.7976 (m-30) REVERT: B 19 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8235 (ptt90) REVERT: B 36 ASN cc_start: 0.8469 (m110) cc_final: 0.8093 (m-40) REVERT: B 134 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: B 260 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: C 294 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8129 (t0) REVERT: G 21 MET cc_start: 0.7637 (mmp) cc_final: 0.7283 (mmp) REVERT: S 3 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7623 (mm110) REVERT: S 18 ARG cc_start: 0.7371 (tpp80) cc_final: 0.6818 (tpp80) REVERT: S 148 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6814 (ttp-170) outliers start: 67 outliers final: 56 residues processed: 211 average time/residue: 0.2320 time to fit residues: 65.5606 Evaluate side-chains 219 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 159 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 0.1980 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN C 294 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9033 Z= 0.282 Angle : 0.608 9.726 12243 Z= 0.314 Chirality : 0.043 0.143 1386 Planarity : 0.004 0.052 1554 Dihedral : 5.609 55.921 1238 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 7.89 % Allowed : 32.28 % Favored : 59.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1120 helix: 2.54 (0.28), residues: 355 sheet: -0.57 (0.32), residues: 281 loop : -1.67 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 50 HIS 0.006 0.001 HIS A 184 PHE 0.013 0.001 PHE B 241 TYR 0.019 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 159 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.9214 (t0) cc_final: 0.8512 (m-30) REVERT: A 290 ASP cc_start: 0.8244 (m-30) cc_final: 0.7970 (m-30) REVERT: B 36 ASN cc_start: 0.8472 (m110) cc_final: 0.8086 (m-40) REVERT: B 130 GLU cc_start: 0.8787 (mp0) cc_final: 0.8535 (mp0) REVERT: B 134 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8139 (ptp90) REVERT: B 260 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: B 338 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8410 (mm) REVERT: C 294 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8329 (t0) REVERT: G 21 MET cc_start: 0.7629 (mmp) cc_final: 0.7246 (mmp) REVERT: S 3 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7625 (mm110) REVERT: S 18 ARG cc_start: 0.7443 (tpp80) cc_final: 0.6306 (ttp80) REVERT: S 148 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6795 (ttp-170) outliers start: 75 outliers final: 62 residues processed: 215 average time/residue: 0.2283 time to fit residues: 66.0491 Evaluate side-chains 224 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4323 > 50: distance: 93 - 94: 5.897 distance: 93 - 96: 3.866 distance: 94 - 95: 10.123 distance: 94 - 99: 6.476 distance: 96 - 98: 6.565 distance: 99 - 100: 7.055 distance: 100 - 101: 13.253 distance: 101 - 102: 12.964 distance: 101 - 103: 8.735 distance: 103 - 104: 4.909 distance: 104 - 105: 8.627 distance: 104 - 107: 5.252 distance: 105 - 115: 7.557 distance: 107 - 108: 4.021 distance: 108 - 109: 6.885 distance: 109 - 111: 4.633 distance: 111 - 113: 4.066 distance: 112 - 113: 4.745 distance: 113 - 114: 4.796 distance: 115 - 116: 4.599 distance: 116 - 117: 17.199 distance: 116 - 119: 6.868 distance: 117 - 118: 4.609 distance: 117 - 123: 7.839 distance: 119 - 120: 12.396 distance: 120 - 121: 7.706 distance: 120 - 122: 10.618 distance: 123 - 124: 6.504 distance: 124 - 125: 15.917 distance: 124 - 127: 24.090 distance: 125 - 126: 15.351 distance: 125 - 129: 12.477 distance: 127 - 128: 11.535 distance: 129 - 130: 6.415 distance: 129 - 211: 13.638 distance: 130 - 131: 4.599 distance: 131 - 132: 5.681 distance: 131 - 135: 8.921 distance: 132 - 208: 23.141 distance: 135 - 136: 18.616 distance: 136 - 137: 6.690 distance: 136 - 139: 8.576 distance: 137 - 138: 17.756 distance: 137 - 141: 8.654 distance: 139 - 140: 11.624 distance: 141 - 142: 17.143 distance: 141 - 199: 11.537 distance: 142 - 143: 7.607 distance: 142 - 145: 19.794 distance: 143 - 144: 8.005 distance: 143 - 152: 13.174 distance: 144 - 196: 20.170 distance: 145 - 146: 13.153 distance: 146 - 147: 16.038 distance: 147 - 148: 9.137 distance: 148 - 149: 18.779 distance: 149 - 150: 20.654 distance: 149 - 151: 23.202 distance: 152 - 153: 18.583 distance: 153 - 154: 14.968 distance: 153 - 156: 14.106 distance: 154 - 155: 5.329 distance: 154 - 163: 12.636 distance: 156 - 157: 6.240 distance: 157 - 158: 30.308 distance: 157 - 159: 24.302 distance: 158 - 160: 14.925 distance: 159 - 161: 23.594 distance: 160 - 162: 15.663 distance: 161 - 162: 33.896 distance: 163 - 164: 15.062 distance: 164 - 165: 23.272 distance: 164 - 167: 19.069 distance: 165 - 166: 15.209 distance: 165 - 171: 14.733 distance: 168 - 169: 16.372 distance: 168 - 170: 15.236